Almost any of the brands out there make "low profile" tool boxes. I prefer the cross bed type where the edges rest on top of the truck bed rails. My current box is a little over 2 1/2" from the top of the bed rail to the top of the lid.......certainly no clearance issues there. You can find them all the way from say $200 up to over $1000 dollars and it just depends on the material used to make it, the quality of the construction, and the features/locks that they use. Do a google search for low profile crossbed tool box and you'll be amazed at how many pop up. Then of course you can find the kind that just mount to the bed of the truck and don't sit on the bed rails....it all about personal preference.
Ditto @xrated. I have the over the bed rails side to side type in my short bed truck with a 5th wheel. Works well....I also have a slider type hitch that with the new(ish) trailer I don't have to slide even on near 90 degree turns.
I do have good clearance between the tailer and the bed rails - 5" or so......leaves some breathing room.
It has never interfered with my 5th wheel and it sets about 6 inches above the floor of the bed. When the hitch is removed a sheet of plywood or Sheetrock will fit under the tool box making it easier to haul them.